VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Oct 23 2019 - 13:07:18 CDT

Could you explain a bit further why you can't use the built-in plugin? I've used the plugin for NPT simulations before, and it has never cared what the box volume is or if it changes. All the plugin does is look at the loaded trajectory to see how many pairs there are within each histogram bin. That seems to be exactly what you want to do, so I'm a bit puzzled what you'd like VMD to do differently.

-Josh

On 2019-10-23 11:40:45-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:

I would like to plot RDFs for molecular dynamics simulation results. The simulations ran in the NPT ensemble. This means that I can't use VMD's GUI for plotting RDFs available at Extensions/Analysis/Radial Pair Distribution Function. I have a different cell volume/parameter at each time step, but the GUI only allows a single cell volume.
I have spent a couple of months trying to find other software that can do this and have had no success, either because I can't access software that can do it or it has not been possible to find out how to do what I need.
Does anyone know if there is a way to do this in VMD? I am stuck. If there is, I would be very grateful for any newbie-level advice. I have two relevant files. (1) My cell volume/parameter files are in XYZ format (three columns) and my cells have 90 degree angles. (2) My trajectory files have the following format:

 1000

 i = 0, time = 0.000, E = -1862.5354785273

 Mg 2.7122680189 11.0569574242 6.8765696187

 Mg 1.7122680189 7.0569574242 2.8765696187

 Mg 9.8778827417 5.5336942397 3.4088988234

Thank you.